Remember that word count is for every single file in the ePub that is in the manifest. Frequently books include chapters of upcoming releases and all sorts of other cruft. Use Tweak ePub, open each HTML page in a browser, paste into word and get it to do a word count if you don't believe it. Just don't cheat and skip any pages...

Oops, sorry, I wasn't clear. The issue is that it is UNDERcounting. It's giving a wordcount of around 9k for a book that's probably closer to 100k...